Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: SGCA vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000023.4(SGCA):c.1120C>T (p.Arg374Cys)

CA180427

167678 (ClinVar)

Gene: SGCA
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: c7a196fd-7143-4cc2-8e0e-04b6fb297cfe
Approved on: 2025-06-24
Published on: 2025-07-08

HGVS expressions

NM_000023.4:c.1120C>T
NM_000023.4(SGCA):c.1120C>T (p.Arg374Cys)
NC_000017.11:g.50175393C>T
CM000679.2:g.50175393C>T
NC_000017.10:g.48252754C>T
CM000679.1:g.48252754C>T
NC_000017.9:g.45607753C>T
NG_008889.1:g.14389C>T
ENST00000504307.3:n.547-3216G>A
ENST00000504073.2:c.970C>T
ENST00000504307.2:n.492-3216G>A
ENST00000511303.6:n.455+18C>T
ENST00000682109.1:c.1000C>T
ENST00000683226.1:n.1718C>T
ENST00000683294.1:c.*223C>T
ENST00000683544.1:n.774C>T
ENST00000262018.8:c.1120C>T
ENST00000262018.7:c.1120C>T
ENST00000344627.10:c.748C>T
ENST00000504073.1:c.437C>T
ENST00000504307.1:n.470-3216G>A
ENST00000505964.1:n.221C>T
ENST00000508382.1:n.165C>T
ENST00000511303.5:c.451+18C>T
ENST00000513821.5:c.*14C>T
ENST00000513942.5:n.539C>T
NM_000023.2:c.1120C>T
NM_001135697.1:c.748C>T
NM_000023.3:c.1120C>T
NM_001135697.2:c.748C>T
NR_135553.1:n.967C>T
NM_001135697.3:c.748C>T
NR_135553.2:n.947C>T
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 1
BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SGCA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_000023.4: c.1120C>T variant in SGCA is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 374, p.(Arg374Cys). The filtering allele frequency of this variant for gnomAD v4.1.0 exomes is 0.01775 (the lower threshold of the 95% CI of 63/33478 African/African American chromosomes), which is higher than the ClinGen LGMD VCEP threshold (>0.002) for BA1, and therefore meets this criterion (BA1). This variant is not located in a splice region, and the SpliceAI score is 0, which suggests it does not impact splicing. The computational predictor REVEL gives a score of 0.39, which is above the LGMD VCEP threshold predicting a benign impact on SGCA function (≤0.1; BP4 not met). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 1.0.0; 06/24/2025): BA1.
Met criteria codes
BA1
The filtering allele frequency of this variant is 0.01775 for gnomAD v4.1.0 exomes (the lower threshold of the 95% CI of 63/33478 African/African American chromosomes), which is higher than the ClinGen LGMD VCEP threshold (>0.002) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
BP4
The SpliceAI score for this variant is 0, which suggests it does not impact splicing and is below the LGMD VCEP threshold of ≤0.05. The computational predictor REVEL gives a score of 0.39, which is above the LGMD VCEP threshold predicting a benign impact on SGCA function (≤0.1; BP4 not met).
Curation History
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